A ship’s radiated acoustic signature is known after a range measurement, but it changes from that the longer the ship is in-service. The Ship Signatures Management System (SSMS) provides an organic, real-time capability for a naval ship to monitor its own signature in order to evaluate the impact of proposed actions on its counter-detection range and sensor performance. Ship protection is enhanced through insightful and timely signature data. In particular, this paper discusses the tonal detection and tracking algorithms used to monitor on-board machinery and propeller activity. The paper specifically addresses tonals that appear or disappear as a consequence of changes in the background level, as well as that of crossed tonals. This is of significance because it impacts the SSMS’s ability to attribute cause to changes in the ship acoustic signature. In particular, it is impossible to associate tonals that are time synchronized in their frequency and intensity changes as being created by a single cause (e.g., piece of machinery) with a known tonal set. The use of tonal amplitude and the cause for the signal-to-noise ratio change, in addition to the signal-to-noise ratio, remedies the detection and tracking of tonals that appear/disappear relative to the background. The additional use of tonal width is suggested as a means to remedy the problem of crossed tonals.